Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001061.1 Kokia drynarioides strain JFW-HI SEQ_112310, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24675
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:991 original size:279 final size:280
Alignment explanation
Indices: 436--3527 Score: 3175
Period size: 279 Copynumber: 11.0 Consensus size: 280
426 TTCGATAGTG
* *
436 GGGAGATTCTTCTTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGTCAATTTGAATG
1 GGGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATG
** * * * *
501 CTGTGAA-AAAATAAGAATA-A-GGACCAAAT-CTGCGCGAATCAGTAAGTACAAGGACTATTCT
66 CT-ACAAGTAAATAAAAATAGAGGGACCAAATCCT-CGCAAATCAATAAGTACAAGGACTATTCT
* * * * *
562 TAGAATTTGTA-CTAAAATAATATTTGTTTCACTTGACTCTGAAACGCGAAGATCTTGATATAAA
129 TAGAATTT-AACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATATAAA
* * * * * * *
626 CAATAATATATAT-TTTTTTATCTTAAAACTGTCATATTACACGGCGGTTTCAAGATAATTGTAT
193 AAATAA-A-ATTTCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCAT
*
690 GTGACTGAGGTGCTTGTATTTGGCA
256 GTGACTGAGCTGCTTGTATTTGGCA
* * * *
715 GGGATATTCTTCGTTGATTTCATCAATTTTCTTTCTTTTCTCAAACTTAAGACTCCAATTTGAAT
1 GGGAGATTCTTCGTTGATTTCATCGATTTTGTTT-TTTTCTCAAACTTAAGACGCCAATTTGAAT
* *
780 TCTACAAGTAAAT-AAAATAGAGGGATCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCTT
65 GCTACAAGTAAATAAAAATAGAGGGACCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCTT
* ** * *
844 AGAATTTAACCTAAAATAATGTTTGTTTCTTTCGACCCTGACACTCGACGTTCTTGATATAAAAA
130 AGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATATAAAAA
* ** * * * *
909 A-AAAATTTCATTTTTATTTTAAAGTTGCCATCTTACGCGGCGGTTTCAGGATAATTGCATGTAA
195 ATAAAATTTCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTGA
973 CTGAGCTGCTTGTATTTGGCA
260 CTGAGCTGCTTGTATTTGGCA
* * * * *
994 AGGAAATTCTTCTTTGATTTCATTGATTTTGTTTTTTTCTCAAACTTAAGACCCCAATTTGAATG
1 GGGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATG
* * * * *
1059 CTACGAA-AAAATAAAAATAGATGGACCAAATCCTTGCAAATCAATAAGTACAATGATTATTCTT
66 CTAC-AAGTAAATAAAAATAGAGGGACCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCTT
* * * * * *
1123 AGAATTTAACCTAAAATTATAATTGTTTCACTCGACTCAGACATGTGGCGTTCTTGATATAAAAA
130 AGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATATAAAAA
* ******* * ** * * * * * *
1188 ATAATAGAAAAAGTTTACTTTAAAACAACCATTTTAGGCAGTTGTTTTAAGATAATTACATGTGA
195 ATAAAATTTCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTGA
* *
1253 CTGGGTTGCTTGTATTTGGCA
260 CTGAGCTGCTTGTATTTGGCA
* * * * *
1274 AGGAGATACTTCGTTGATTTCATCAATTTTGTTTTTTTCTCAAACCTAAGAGGCCAATTTGAATG
1 GGGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATG
* *
1339 CTA-AGAGTAAACAAAAATAGAGGGACCAAATCCGT-GCAAATAAATAAGTACAAGGACTATTCT
66 CTACA-AGTAAATAAAAATAGAGGGACCAAATCC-TCGCAAATCAATAAGTACAAGGACTATTCT
* * * * *
1402 TAGAATTTAACCTAAAATAATATTTGTTTCA-TCAACTCTAACACCCGGCATTCTTGATATAAAA
129 TAGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATATAAAA
* * * *
1466 AATAATAAATTCTTTTTTTATCTTAAAACTGCCATATTACGCGGCGGTTTCAAGTTAATTGCATG
194 AATAA-AATTTC-TTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATG
** *
1531 TGACTGAGCTATTTGTATTTAGCA
257 TGACTGAGCTGCTTGTATTTGGCA
* * * * * * *
1555 AGGAGATTCTTGGTTGATTTCATCAATTTTATTTTTTTTCTAAAACATAAGACACCAATTTGAAT
1 GGGAGATTCTTCGTTGATTTCATCGATTTT-GTTTTTTTCTCAAACTTAAGACGCCAATTTGAAT
* * * * *
1620 GCTACGACTAAA-AAAAATAGAGGGATCAAATCCGCGCAAATCAATAAGTATAAGGA-TATTCTT
65 GCTACAAGTAAATAAAAATAGAGGGACCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCTT
* ** * *
1683 AGAATTTAACCTAAACTAATATTTGTTTCTTTTGACTCTGACAAGCGACGTTCTTGATATAAAAG
130 AGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATATAAAA-
* * * * * **** * *
1748 AAT--ATTTTCTATTCTATTTTAAAGCTGCCATATTACTCGAAAATTTGACGATAATTGCATGTG
194 AATAAAATTTCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTG
* *
1811 ACAGAAG-TGCTTGTATTTGGCG
259 ACTG-AGCTGCTTGTATTTGGCA
* *
1833 GGGAGATTCTTCTTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGATGCCAATTTGAATG
1 GGGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATG
* * *
1898 CTA-AGAATAAATAAAAAATAGAGGGACCAAATCCGT-GCAAATCAGTAGGTACAAGGACTATTC
66 CTACA-AGTAAAT-AAAAATAGAGGGACCAAATCC-TCGCAAATCAATAAGTACAAGGACTATTC
* * * * ** *
1961 TTAGAATTTAAACTAAAATAAT-TTTTTTTCACTCGAATCTAACATTCGGCGTTCTTGATA-AAA
128 TTAGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATATAAA
* * * * * * * * * * ** * *
2024 AAATAATATTTTTTTTTTATCTTAAAACTTCTATCTTAAGTGTTGGTTTCAAGAGAGCTCCTTGT
193 AAATAAAATTTCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGT
* * *
2089 GATTGAGCTGCTTGT-TTTCTGAA
258 GACTGAGCTGCTTGTATTT-GGCA
* * * *
2112 GGGAGATTCTTCATTGATTTCATCAATTTT-ATTTTTTCTCAAACGTAAGA-GCCCAACTTT-AA
1 GGGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACG-CCAA-TTTGAA
* * ** *
2174 TGCTACAAGTAAATAAAAATAGAGGGACCAAATTCTCACAAATCAATAAGTATGAGGCCTATTCT
64 TGCTACAAGTAAATAAAAATAGAGGGACCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCT
* * * * *
2239 TAGAATTTAACCTAAAATAAT-TTT-TTTCCACACGACACTAACACGTGATGTTCTTGATATAAA
129 TAGAATTTAACCTAAAATAATATTTGTTT-CACTCGACTCTGACACGCGACGTTCTTGATATAAA
** * * * * ** * *
2302 AAATAATAAACTCTTTTGTTATCTTAAAACTTCCATCTTAAGTTGTGGTTTTAAGATAATTTCAT
193 AAATAA-AATTTCTTTT-TTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCAT
2367 GTGACTGAGCTGCTTGTATTTGGCA
256 GTGACTGAGCTGCTTGTATTTGGCA
* * *
2392 GAGAGATTCTTCTTTGATTTCATCGATTTTGTTTTTTTTCTCAAATTTGAAGACGCCAATTTGAA
1 GGGAGATTCTTCGTTGATTTCATCGATTTTG-TTTTTTTCTCAAACTT-AAGACGCCAATTTGAA
* * * * * * *
2457 TGCTACGAGTAAATAAAAATATAGGGACCAAATCCACGGAAATCAATAAGAATAAGGATTATTCT
64 TGCTACAAGTAAATAAAAATAGAGGGACCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCT
** * *
2522 TAGAATTTAACCTAAAATAATATTTGTTTCTTTCGACTCTAACACGCGGCGTTCTTGATATAAAA
129 TAGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATAT-AAA
* * * * *
2587 AAATAATAATTTCTTTTTTATTTGAAAACTGCCATCTTACGCGGCGGTTTCAAAATAATTGTATG
193 AAATAA-AATTTCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATG
* *
2652 TAACTGAGCTGCTTGTATTTGGAA
257 TGACTGAGCTGCTTGTATTTGGCA
* * * *
2676 GGAAGATTCTT-GTTTTATTTCATTGA--TT-TTTTTTTCTCAAACTTAAGAGGCCAATTTGAAT
1 GGGAGATTCTTCG-TTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAAT
** * * * * *
2737 GCTACAAGTAAATAAAAATAGACAGACCAAATCCGCGCAAATCCACAAGTACAAGTACTTTTCTT
65 GCTACAAGTAAATAAAAATAGAGGGACCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCTT
* * *
2802 ACAATTTAACCTAAAATAATATTTGTTTCACTGGACTCTGATACGCGACGTTCTTGATA-AAAAA
130 AGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATATAAAAA
* * * *
2866 ATAATAAATTCTATTTTTTATCTTAAAACTGCCATATTACACGATGGTTTCAAGATAATTGCATG
195 AT-A-AAATT-TCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATG
* *
2931 TGTCTGAGCTGTTTGTATTTGGCA
257 TGACTGAGCTGCTTGTATTTGGCA
* * * *
2955 GGGAGATTCTTCTTTGATTTCATCGATTTTGTCTTTTTCTCAAACTTAAGAGGCTAATTTGAATG
1 GGGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATG
* * *
3020 CTACGAGTAAATAAATATAGAGGGACCAAATCCGCGCAAATCAATAAGTACATA-GACTATTCTT
66 CTACAAGTAAATAAAAATAGAGGGACCAAATCCTCGCAAATCAATAAGTACA-AGGACTATTCTT
* * *
3084 AGTATTTAACCTAAAATAATATTTGTTTTACTCGACTCTGACACGCGAAGTTCTTGATATAAAAA
130 AGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATATAAAAA
* * * * * *
3149 ATAATAAATTATTTTTTATCTTAAAACTGCCATATTACACAGTGGTTTCAAGATAATTGTATGTG
195 ATAA-AATTTCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTG
*
3214 ACTGAGGTGCTTGTATTTGGCA
259 ACTGAGCTGCTTGTATTTGGCA
* * ********* * *
3236 GGGAGATTCTTTGTTGATTTCTTC-AAAAAAAAAATTTGTCATACTTAAGACGCCAATTTGAATG
1 GGGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATG
* ** * * * *
3300 CTACGAGTAAATAAAAATAGAGGGATTAAATCCGCACAAATCAATAAATTCAAGGACTATTCTTA
66 CTACAAGTAAATAAAAATAGAGGGACCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCTTA
* * * * *
3365 GAATTTAACCTAAAATAAGATATGATTCAGTC-AGCACT-ATCACGC-AGCGTTCTTGATATAAA
131 GAATTTAACCTAAAATAATATTTGTTTCACTCGA-CTCTGA-CACGCGA-CGTTCTTGATATAAA
* * * * *
3427 AAATAATAAATTT-TTTTTTATCTTAAAAATGCCATATTAAGCGGTGATTTCAAGATAATTTCAT
193 AAAT-A-AAATTTCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCAT
*
3491 GTGACTGAGTTGCTTGTATTTGGCAA
256 GTGACTGAGCTGCTTGTATTTGGC-A
3517 GGG-GATTCTTC
1 GGGAGATTCTTC
3528 TTTTTCAACA
Statistics
Matches: 2336, Mismatches: 412, Indels: 129
0.81 0.14 0.04
Matches are distributed among these distances:
276 4 0.00
277 137 0.06
278 181 0.08
279 634 0.27
280 605 0.26
281 347 0.15
282 205 0.09
283 94 0.04
284 108 0.05
285 21 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (280 bp):
GGGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATG
CTACAAGTAAATAAAAATAGAGGGACCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCTTA
GAATTTAACCTAAAATAATATTTGTTTCACTCGACTCTGACACGCGACGTTCTTGATATAAAAAA
TAAAATTTCTTTTTTATTTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTGAC
TGAGCTGCTTGTATTTGGCA
Found at i:1358 original size:280 final size:279
Alignment explanation
Indices: 437--3527 Score: 3105
Period size: 280 Copynumber: 11.0 Consensus size: 279
427 TCGATAGTGG
* *
437 GGAGATTCTTCTTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGTCAATTTGAATGC
1 GGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATGC
** ** * * * *
502 TGTGAAAAAATAAGAATA-A-GGACCAAATCTGCGCGAATCAGTAAGTACAAGGACTATTCTTAG
66 TAAGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCTTAG
* * * * * * *
565 AATTTGTA-CTAAAATAATATTTGTTTCACTTGACTCTGAAACGCGAAGATCTTGATATAAACAA
131 AATTT-AACCTAAAATAATATTTGTTTCACTCGACTCAGACACGCGACGTTCTTGATATAAAAAA
* * * * *
629 TAATATATATTTTTTTATCTTAAAACTGTCATATTACACGGCGGTTTCAAGATAATTGTATGTGA
195 TAATA-A-ACTTTTTTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTGA
* *
694 CTGAGGTGCTTGTATTTGGCAG
258 CTGAGCTGCTTGTATTTGGCAA
* * * * *
716 GGATATTCTTCGTTGATTTCATCAATTTTCTTTCTTTTCTCAAACTTAAGACTCCAATTTGAATT
1 GGAGATTCTTCGTTGATTTCATCGATTTTGTTT-TTTTCTCAAACTTAAGACGCCAATTTGAATG
* *
781 CTACA-AGTAAAT-AAAATAGAGGGATCAAATCCTCGCAAATCAATAAGTACAAGGACTATTCTT
65 CTA-AGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCTT
* ** * * *
844 AGAATTTAACCTAAAATAATGTTTGTTTCTTTCGACCCTGACACTCGACGTTCTTGATATAAAAA
129 AGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCAGACACGCGACGTTCTTGATATAAAAA
* * * ** * * * *
909 A-AA-AATTTCATTTTTATTTTAAAGTTGCCATCTTACGCGGCGGTTTCAGGATAATTGCATGTA
194 ATAATAA--ACTTTTTTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTG
972 ACTGAGCTGCTTGTATTTGGCAA
257 ACTGAGCTGCTTGTATTTGGCAA
* * * *
995 GGAAATTCTTCTTTGATTTCATTGATTTTGTTTTTTTCTCAAACTTAAGACCCCAATTTGAATGC
1 GGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATGC
* ** * ** * *
1060 TACGAAAAAATAAAAATAGATGGACCAAATCCTTGCAAATCAATAAGTACAATGATTATTCTTAG
66 TAAGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCTTAG
* * * * *
1125 AATTTAACCTAAAATTATAATTGTTTCACTCGACTCAGACATGTGGCGTTCTTGATATAAAAAAT
131 AATTTAACCTAAAATAATATTTGTTTCACTCGACTCAGACACGCGACGTTCTTGATATAAAAAAT
**** ** * * * * * *
1190 AATAGAAAAAGTTTA-CTTTAAAACAACCATTTTAGGCAGTTGTTTTAAGATAATTACATGTGAC
196 AATA-AACTTTTTTATC-TTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTGAC
* *
1254 TGGGTTGCTTGTATTTGGCAA
259 TGAGCTGCTTGTATTTGGCAA
* * * *
1275 GGAGATACTTCGTTGATTTCATCAATTTTGTTTTTTTCTCAAACCTAAGAGGCCAATTTGAATGC
1 GGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATGC
* * *
1340 TAAGAGTAAACAAAAATAGAGGGACCAAATCCGTGCAAATAAATAAGTACAAGGACTATTCTTAG
66 TAAGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCTTAG
* * * *
1405 AATTTAACCTAAAATAATATTTGTTTCA-TCAACTCTA-ACACCCGGCATTCTTGATATAAAAAA
131 AATTTAACCTAAAATAATATTTGTTTCACTCGACTC-AGACACGCGACGTTCTTGATATAAAAAA
* *
1468 TAATAAATTCTTTTTTTATCTTAAAACTGCCATATTACGCGGCGGTTTCAAGTTAATTGCATGTG
195 TAATAAA--C-TTTTTTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTG
** *
1533 ACTGAGCTATTTGTATTTAGCAA
257 ACTGAGCTGCTTGTATTTGGCAA
* * * * * *
1556 GGAGATTCTTGGTTGATTTCATCAATTTTATTTTTTTTCTAAAACATAAGACACCAATTTGAATG
1 GGAGATTCTTCGTTGATTTCATCGATTTT-GTTTTTTTCTCAAACTTAAGACGCCAATTTGAATG
* * * *
1621 CTACGACTAAA-AAAAATAGAGGGATCAAATCCGCGCAAATCAATAAGTATAAGGA-TATTCTTA
65 CTAAGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCTTA
* ** * * *
1684 GAATTTAACCTAAACTAATATTTGTTTCTTTTGACTCTGACAAGCGACGTTCTTGATATAAAAGA
130 GAATTTAACCTAAAATAATATTTGTTTCACTCGACTCAGACACGCGACGTTCTTGATATAAAA-A
*** * * * * * **** * *
1749 AT-ATTTTCTATTCTATTTTAAAGCTGCCATATTACTCGAAAATTTGACGATAATTGCATGTGAC
194 ATAATAAACTTTTTTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTGAC
* **
1813 AGAAG-TGCTTGTATTTGGCGG
259 TG-AGCTGCTTGTATTTGGCAA
* *
1834 GGAGATTCTTCTTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGATGCCAATTTGAATGC
1 GGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATGC
* * * *
1899 TAAGAATAAATAAAAAATAGAGGGACCAAATCCGTGCAAATCAGTAGGTACAAGGACTATTCTTA
66 TAAGAGTAAAT-AAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCTTA
* * * ** *
1964 GAATTTAAACTAAAATAAT-TTTTTTTCACTCGAATCTA-ACATTCGGCGTTCTTGATA-AAAAA
130 GAATTTAACCTAAAATAATATTTGTTTCACTCGACTC-AGACACGCGACGTTCTTGATATAAAAA
*** * * * * * * * ** * *
2026 ATAATATTTTTTTTTTATCTTAAAACTTCTATCTTAAGTGTTGGTTTCAAGAGAGCTCCTTGTGA
194 ATAATA-AACTTTTTTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTGA
* *
2091 TTGAGCTGCTTGT-TTTCTG-AA
258 CTGAGCTGCTTGTATTT-GGCAA
* * * *
2112 GGGAGATTCTTCATTGATTTCATCAATTTT-ATTTTTTCTCAAACGTAAGA-GCCCAACTTT-AA
1 -GGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACG-CCAA-TTTGAA
* * * ** *
2174 TGCTACA-AGTAAATAAAAATAGAGGGACCAAATTCTCACAAATCAATAAGTATGAGGCCTATTC
63 TGCTA-AGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTC
* * * *
2238 TTAGAATTTAACCTAAAATAAT-TTT-TTTCCACACGACACTA-ACACGTGATGTTCTTGATATA
127 TTAGAATTTAACCTAAAATAATATTTGTTT-CACTCGACTC-AGACACGCGACGTTCTTGATATA
* * * ** * *
2300 AAAAATAATAAACTCTTTTGTTATCTTAAAACTTCCATCTTAAGTTGTGGTTTTAAGATAATTTC
190 AAAAATAATAAA--CTTTT-TTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGC
2365 ATGTGACTGAGCTGCTTGTATTTGGC-A
252 ATGTGACTGAGCTGCTTGTATTTGGCAA
* *
2392 GAGAGATTCTTCTTTGATTTCATCGATTTTGTTTTTTTTCTCAAATTTGAAGACGCCAATTTGAA
1 G-GAGATTCTTCGTTGATTTCATCGATTTTG-TTTTTTTCTCAAACTT-AAGACGCCAATTTGAA
* * * * * * *
2457 TGCTACGAGTAAATAAAAATATAGGGACCAAATCCACGGAAATCAATAAGAATAAGGATTATTCT
63 TGCTAAGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCT
** *
2522 TAGAATTTAACCTAAAATAATATTTGTTTCTTTCGACTCTA-ACACGCGGCGTTCTTGATATAAA
128 TAGAATTTAACCTAAAATAATATTTGTTTCACTCGACTC-AGACACGCGACGTTCTTGATAT-AA
* * * * *
2586 AAAATAATAATTTCTTTTTTAT-TTGAAAACTGCCATCTTACGCGGCGGTTTCAAAATAATTGTA
191 AAAATAATAA--ACTTTTTTATCTT-AAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCA
*
2650 TGTAACTGAGCTGCTTGTATTTGG-AA
253 TGTGACTGAGCTGCTTGTATTTGGCAA
* * *
2676 GGAAGATTCTT-GTTTTATTTCATTGA--TT-TTTTTTTCTCAAACTTAAGAGGCCAATTTGAAT
1 GG-AGATTCTTCG-TTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAAT
** * * * *
2737 GCTACA-AGTAAATAAAAATAGACAGACCAAATCCGCGCAAATCCACAAGTACAAGTACTTTTCT
64 GCTA-AGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCT
* * * *
2801 TACAATTTAACCTAAAATAATATTTGTTTCACTGGACTCTGATACGCGACGTTCTTGATA-AAAA
128 TAGAATTTAACCTAAAATAATATTTGTTTCACTCGACTCAGACACGCGACGTTCTTGATATAAAA
* *
2865 AATAATAAATTCTATTTTTTATCTTAAAACTGCCATATTACACGATGGTTTCAAGATAATTGCAT
193 AATAATAAA--C--TTTTTTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCAT
* * *
2930 GTGTCTGAGCTGTTTGTATTTGGCAG
254 GTGACTGAGCTGCTTGTATTTGGCAA
* * * *
2956 GGAGATTCTTCTTTGATTTCATCGATTTTGTCTTTTTCTCAAACTTAAGAGGCTAATTTGAATGC
1 GGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATGC
* *
3021 TACGAGTAAATAAATATAGAGGGACCAAATCCGCGCAAATCAATAAGTACATA-GACTATTCTTA
66 TAAGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACA-AGGACTATTCTTA
* * * *
3085 GTATTTAACCTAAAATAATATTTGTTTTACTCGACTCTGACACGCGAAGTTCTTGATATAAAAAA
130 GAATTTAACCTAAAATAATATTTGTTTCACTCGACTCAGACACGCGACGTTCTTGATATAAAAAA
* * * *
3150 TAATAAATTATTTTTTATCTTAAAACTGCCATATTACACAGTGGTTTCAAGATAATTGTATGTGA
195 TAATAAA--CTTTTTTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTGA
* *
3215 CTGAGGTGCTTGTATTTGGCAG
258 CTGAGCTGCTTGTATTTGGCAA
* * ********* * *
3237 GGAGATTCTTTGTTGATTTCTTC-AAAAAAAAAATTTGTCATACTTAAGACGCCAATTTGAATGC
1 GGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATGC
* ** * * *
3301 TACGAGTAAATAAAAATAGAGGGATTAAATCCGCACAAATCAATAAATTCAAGGACTATTCTTAG
66 TAAGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCTTAG
* * * * *
3366 AATTTAACCTAAAATAAGATATGATTCAGTCAGCACT-A-TCACGC-AGCGTTCTTGATATAAAA
131 AATTTAACCTAAAATAATATTTGTTTCACTC-G-ACTCAGACACGCGA-CGTTCTTGATATAAAA
* * * * *
3428 AATAATAAATTTTTTTTTATCTTAAAAATGCCATATTAAGCGGTGATTTCAAGATAATTTCATGT
193 AATAATAAA--CTTTTTTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGT
*
3493 GACTGAGTTGCTTGTATTTGGCAA
256 GACTGAGCTGCTTGTATTTGGCAA
*
3517 GGGGATTCTTC
1 GGAGATTCTTC
3528 TTTTTCAACA
Statistics
Matches: 2333, Mismatches: 403, Indels: 151
0.81 0.14 0.05
Matches are distributed among these distances:
276 3 0.00
277 144 0.06
278 179 0.08
279 615 0.26
280 619 0.27
281 339 0.15
282 203 0.09
283 104 0.04
284 107 0.05
285 20 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (279 bp):
GGAGATTCTTCGTTGATTTCATCGATTTTGTTTTTTTCTCAAACTTAAGACGCCAATTTGAATGC
TAAGAGTAAATAAAAATAGAGGGACCAAATCCGCGCAAATCAATAAGTACAAGGACTATTCTTAG
AATTTAACCTAAAATAATATTTGTTTCACTCGACTCAGACACGCGACGTTCTTGATATAAAAAAT
AATAAACTTTTTTATCTTAAAACTGCCATATTACGCGGTGGTTTCAAGATAATTGCATGTGACTG
AGCTGCTTGTATTTGGCAA
Found at i:10004 original size:31 final size:31
Alignment explanation
Indices: 9969--10038 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
9959 AATCATTTAG
*
9969 TTAAATTAAGG-GTAAATTGCACTATTAGTCA
1 TTAAATTAAGGAGTAAATTGCAAT-TTAGTCA
* *
10000 TTAAATT-AGGAGTAAGTTTCAATTTAGTCA
1 TTAAATTAAGGAGTAAATTGCAATTTAGTCA
*
10030 TTTAATTAA
1 TTAAATTAA
10039 AAAAAGTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (31 bp):
TTAAATTAAGGAGTAAATTGCAATTTAGTCA
Found at i:10103 original size:31 final size:31
Alignment explanation
Indices: 10059--10119 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
10049 AATTTGACCA
*
10059 CTAAACAATTCAAAAGT-TTTCATTTAAGTCT
1 CTAAACAACTCAAAA-TATTTCATTTAAGTCT
* *
10090 CTAAACTACTCAAAATATTTTATTTAAGTC
1 CTAAACAACTCAAAATATTTCATTTAAGTC
10120 ATTGGATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (31 bp):
CTAAACAACTCAAAATATTTCATTTAAGTCT
Found at i:10510 original size:94 final size:94
Alignment explanation
Indices: 10393--10582 Score: 337
Period size: 94 Copynumber: 2.0 Consensus size: 94
10383 ACACACACAC
*
10393 ATATATATCATTGTGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAACAT
1 ATATATATCATTGCGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAACAT
* *
10458 ATTTGATGAGTTTCTCGATTGTAATATAT
66 ATTTGATGAGTTTCTCCATTGTAATAAAT
10487 ATATATAT-ATATGCGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAACA
1 ATATATATCAT-TGCGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAACA
10551 TATTTGATGAGTTTCTCCATTGTAATAAAT
65 TATTTGATGAGTTTCTCCATTGTAATAAAT
10581 AT
1 AT
10583 TTGGTTCAAA
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 2 0.02
94 90 0.98
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (94 bp):
ATATATATCATTGCGTTAGCTTTAAATATTTGTCAAAAGATCAACTTGCTTGCTTGATTTAACAT
ATTTGATGAGTTTCTCCATTGTAATAAAT
Found at i:17019 original size:92 final size:98
Alignment explanation
Indices: 16911--17103 Score: 247
Period size: 98 Copynumber: 2.0 Consensus size: 98
16901 TCTCTAATAT
* * *
16911 AATTCTTTTTTGGTTAAAATT-TCATTCACAACAGTTTCACG-AT-A-AGTAATAATA-TTTTAT
1 AATTCTTTTTTGGTTAAAATTATC-TCCACAACAATTTCACGAATAATAATAATAATATTTTTAT
*
16971 AACAAGATGACACAATGGGTGAAACCGTTGTATC
65 AACAAGATGACACAATGGGTGAAACCGTCGTATC
*
17005 AATT-TTTTTT-GTTAAAATTATCTCCACAACAATTTCATGATAATAATAATAATAATATTTTTA
1 AATTCTTTTTTGGTTAAAATTATCTCCACAACAATTTCACG--AATAATAATAATAATATTTTTA
* *
17068 TAACAAGATTACACAATGGGTGAAACTGTCGTATC
64 TAACAAGATGACACAATGGGTGAAACCGTCGTATC
17103 A
1 A
17104 CATGGCAGCT
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
92 23 0.27
93 8 0.09
94 4 0.05
95 2 0.02
96 1 0.01
97 9 0.11
98 38 0.45
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37
Consensus pattern (98 bp):
AATTCTTTTTTGGTTAAAATTATCTCCACAACAATTTCACGAATAATAATAATAATATTTTTATA
ACAAGATGACACAATGGGTGAAACCGTCGTATC
Found at i:19738 original size:29 final size:28
Alignment explanation
Indices: 19706--19819 Score: 131
Period size: 29 Copynumber: 3.9 Consensus size: 28
19696 TTCGAGGTCG
*
19706 AAAATAGAGTTTTTGGACA-TTCAGGGGTA
1 AAAATAGAATTTTTGGA-AGTTC-GGGGTA
*
19735 AAAATGGAATTTTTGGAAGTTTCGGGGGTA
1 AAAATAGAATTTTTGGAAG-TTC-GGGGTA
*
19765 AAAATAGAATTTTTAGAAGTTCGAGGGTA
1 AAAATAGAATTTTTGGAAGTTCG-GGGTA
*
19794 AAAATGGAATTTTTGGAAGTTTCGGG
1 AAAATAGAATTTTTGGAAG-TTCGGG
19820 ACCTCAGGCA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
28 2 0.03
29 42 0.57
30 30 0.41
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (28 bp):
AAAATAGAATTTTTGGAAGTTCGGGGTA
Found at i:19765 original size:30 final size:30
Alignment explanation
Indices: 19729--19819 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 30
19719 TGGACATTCA
19729 GGGGTAAAAATGGAATTTTTGGAAGTTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCG
* *
19759 GGGGTAAAAATAGAATTTTTAGAAG-TTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCG
*
19788 AGGGTAAAAATGGAATTTTTGGAAGTTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCG
19818 GG
1 GG
19820 ACCTCAGGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 26 0.48
30 28 0.52
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.32
Consensus pattern (30 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTCG
Found at i:20900 original size:3 final size:3
Alignment explanation
Indices: 20892--20946 Score: 101
Period size: 3 Copynumber: 18.0 Consensus size: 3
20882 AAAGCTACAT
20892 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20940 CTTA TTA
1 -TTA TTA
20947 CAAACAATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:21585 original size:13 final size:13
Alignment explanation
Indices: 21567--21592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21557 TTGGGCTTGA
21567 TTTGTAATTGGAC
1 TTTGTAATTGGAC
21580 TTTGTAATTGGAC
1 TTTGTAATTGGAC
21593 ATTATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:21626 original size:16 final size:16
Alignment explanation
Indices: 21605--21638 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
21595 TATTTAAATA
21605 AATTTAAAATAAACTT
1 AATTTAAAATAAACTT
*
21621 AATTTAAAATAAATTT
1 AATTTAAAATAAACTT
21637 AA
1 AA
21639 ATTTTGTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTTAAAATAAACTT
Found at i:22586 original size:115 final size:115
Alignment explanation
Indices: 22260--22591 Score: 409
Period size: 116 Copynumber: 2.9 Consensus size: 115
22250 ATTTGGTTCA
*
22260 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCAGTATCTCATC
* *
22325 AGGCAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTGATATT
66 AGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTGATATT
* * * *** * * *
22375 CTTCTTTGTATCTCATCAGAAAG-AAGACCGCCTTACTTGTTTCAATCC-GCTTATCTGTATCTC
1 CTTCTCTGTATCTCATCAGGAAGCTA-ACCATTTTA-TTGTTTCGA-CCTGCTTCTCAGTATCTC
* * ** *
22438 ATCAGGAAGTTCGGATTCGAAGATTTTATCACATCGAGCCCTGAGTTGGTATAT
63 ATCAGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTGATAT-T
* * * *
22492 -TTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGGCCTGGTTCTCAGTATCTCATT
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCAGTATCTCATC
*
22556 AGGAAGTTGGGGTTCGAGGATTTGCTCACATCGAGC
66 AGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGC
22592 GTGGGTTTGA
Statistics
Matches: 176, Mismatches: 35, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
114 3 0.02
115 78 0.44
116 91 0.52
117 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (115 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCAGTATCTCATC
AGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTGATATT
Found at i:22894 original size:437 final size:437
Alignment explanation
Indices: 22069--23091 Score: 1505
Period size: 437 Copynumber: 2.3 Consensus size: 437
22059 CCGTATTTCG
* * * *
22069 TCAGGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTATCTTATCAGGAAGTTAGGGTTC
1 TCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTC
* *
22134 GAGGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAAGAAGAT
66 GAGGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
* * *
22199 AACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCCCATCAATAAGACGAATTTGGTTCACTTC
131 GACTGCATCGCTTGTTTCAATCCGCTTCTCTGTATCCCATCAAGAAGACGAATTTGGTTCACTTC
* * * *
22264 TCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGC
196 TCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTACCTCATCAGGA
* * * * *
22329 AGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTGATATTCTTCTTTGTATCTCATCAG
261 AGCTGGGGTTCAAAAATTTGCTCACATCAAGCCCTGAGTAGATATTCTTCTTTATATCTCATCAG
* *
22394 AAAGAAGACCGCCTTACTTGTTTCAATCCGCTTATCTGTATCTCATCAGGAAGTTCGGATTCGAA
326 AAAGAAGACCGCCTTACTTGTTTCAATCCGCTTATCTGTATCTCATCAGAAAGCTCGGATTCGAA
* * *
22459 GATTTTATCACATCGAGCCCTGAGTTGGTATATTTCTCTGTATCTCA
391 GACTTGATCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCA
* * *
22506 TCAGGAAGCTAACCATTTTATTATTTCGGCCTGGTTCTCAGTATCTCATTAGGAAGTTGGGGTTC
1 TCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTC
* *
22571 GAGGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTTTTCTTCTCAGTATCTCATTAGGAAGAT
66 GAGGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
* *
22636 GACTGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGATGAATTTGGTTCACTTC
131 GACTGCATCGCTTGTTTCAATCCGCTTCTCTGTATCCCATCAAGAAGACGAATTTGGTTCACTTC
22701 TCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTACCTCATCAGGA
196 TCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTACCTCATCAGGA
* * * *
22766 AGCTGGGGTTCAAAAATTTGTTCGCATCAAGTCCTGAGTCAG-TATTCTTCTTTATCTCTCATCA
261 AGCTGGGGTTCAAAAATTTGCTCACATCAAGCCCTGAGT-AGATATTCTTCTTTATATCTCATCA
* * * * *
22830 GGAAGATGACCGCCTTACTTGTTTTAATCCGCTTCTCTGTATCTTATCAGAAAGCT-GAGATTCG
325 GAAAGAAGACCGCCTTACTTGTTTCAATCCGCTTATCTGTATCTCATCAGAAAGCTCG-GATTCG
*
22894 AAGACTTGATCACATCGAGCCCTGTGTTGGTATACTTCTCTGTATCTCA
389 AAGACTTGATCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCA
* * *
22943 TCAGGAAGCTAACCATTTTATTATTTTGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTC
1 TCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTC
* * * * ** *
23008 GAAGATTTGCTCACTTTGAGCCTCGTTTCATTTATTTGGTCTTCTTCTCAGTATCTCATCAGGAA
66 GAGGATTTGCTCACATCGAGCGT-GGGT--TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAA
*
23073 TATGA-TCGCATCGC-TGTTT
128 GATGACT-GCATCGCTTGTTT
23092 GTGGATGGTT
Statistics
Matches: 524, Mismatches: 56, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
436 1 0.00
437 471 0.90
438 3 0.01
439 6 0.01
440 43 0.08
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (437 bp):
TCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTC
GAGGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
GACTGCATCGCTTGTTTCAATCCGCTTCTCTGTATCCCATCAAGAAGACGAATTTGGTTCACTTC
TCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTACCTCATCAGGA
AGCTGGGGTTCAAAAATTTGCTCACATCAAGCCCTGAGTAGATATTCTTCTTTATATCTCATCAG
AAAGAAGACCGCCTTACTTGTTTCAATCCGCTTATCTGTATCTCATCAGAAAGCTCGGATTCGAA
GACTTGATCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCA
Found at i:23029 original size:115 final size:115
Alignment explanation
Indices: 22696--23021 Score: 330
Period size: 116 Copynumber: 2.8 Consensus size: 115
22686 AATTTGGTTC
* * * * *
22696 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTACCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTTGACCTGCTTCTCAGTATCTCAT
* * * * * *
22761 CAGGAAGCTGGGGTTCAAAAATTTGTTCGCATCAAGTCCTGAGTCAGTAT
66 CAGGAAGCTGGGGTTCGAAGATTTGATCACATCGAGCCCTGAGTCAGTAT
* * * * * * *** * * *
22811 TCTTCTTTATCTCTCATCAGGAAGATGACCGCCTTACTTGTTTTAATCC-GCTTCTCTGTATCTT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTA-TTGTTTTGA-CCTGCTTCTCAGTATCTC
* * * * * **
22875 ATCAGAAAGCTGAGATTCGAAGACTTGATCACATCGAGCCCTGTGTTGGTAT
64 ATCAGGAAGCTGGGGTTCGAAGATTTGATCACATCGAGCCCTGAGTCAGTAT
* *
22927 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTTGACCTGCTTCTCAATATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTTGACCTGCTTCTCAGTATCTCAT
*
22992 CAGGAAGCTGGGGTTCGAAGATTTGCTCAC
66 CAGGAAGCTGGGGTTCGAAGATTTGATCAC
23022 TTTGAGCCTC
Statistics
Matches: 159, Mismatches: 49, Indels: 6
0.74 0.23 0.03
Matches are distributed among these distances:
114 2 0.01
115 72 0.45
116 83 0.52
117 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (115 bp):
ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTTGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTGGGGTTCGAAGATTTGATCACATCGAGCCCTGAGTCAGTAT
Done.